BLASTP 2.2.18 [Mar-02-2008] Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. Reference for compositional score matrix adjustment: Altschul, Stephen F., John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis, Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109. Query= 0001.3139.p (309 letters) Database: BlastDatabases/689/689 4735 sequences; 1,619,870 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value gi|300312479|ref|YP_003776571.1| dipeptide/oligopeptide/nickel A... 533 e-153 gi|300310894|ref|YP_003774986.1| dipeptide/oligopeptide/nickel A... 193 1e-50 gi|300311171|ref|YP_003775263.1| dipeptide/oligopeptide/nickel A... 181 5e-47 gi|300310465|ref|YP_003774557.1| dipeptide/oligopeptide/nickel A... 114 1e-26 gi|300312717|ref|YP_003776809.1| ABC transporter permease [Herba... 112 5e-26 >gi|300312479|ref|YP_003776571.1| dipeptide/oligopeptide/nickel ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 305 Score = 533 bits (1372), Expect = e-153, Method: Compositional matrix adjust. Identities = 285/293 (97%), Positives = 290/293 (98%) Query: 17 VLQAALPPLPAWRRQLRRLLGHRGLMLGAAVLAVIVLAAIFAPLLAPHDPFDQDVTARLI 76 +LQ ALPPLPAWRR+LRRLLGHRGLM+GAAVLAVIVLAAIFAPLLAPHDPFDQDVTARLI Sbjct: 13 LLQGALPPLPAWRRKLRRLLGHRGLMIGAAVLAVIVLAAIFAPLLAPHDPFDQDVTARLI 72 Query: 77 PPVWQAQGSWEHILGTDKLGRDYLSRLIFGARVSLTIGVAAALISGLIGTTLGVLAGYFG 136 PPVWQAQGSWEHILGTDKLGRDY SRLI+GARVSLTIG+AAALISGLIGTTLGVLAGYFG Sbjct: 73 PPVWQAQGSWEHILGTDKLGRDYFSRLIYGARVSLTIGLAAALISGLIGTTLGVLAGYFG 132 Query: 137 GRTDAVISYLITTRLAMPVVLVALAMASLVGGSLKVVIVLLGLLLWDRFAVVTRSATQQL 196 GRTDAVISYLITTRLAMPVVLVALAMASLVGGSLKVVIVLLGLLLWDRFAVVTRSATQQL Sbjct: 133 GRTDAVISYLITTRLAMPVVLVALAMASLVGGSLKVVIVLLGLLLWDRFAVVTRSATQQL 192 Query: 197 RDAEFIAAAKAIGASTPYILLREILPNIMGALIVVATLEMAHAILLEATLSFLGLGVQPP 256 RDAEFIAAAKAIGASTPYILLREILPNIMGALIVV TLEMAHAILLEATLSFLGLGVQPP Sbjct: 193 RDAEFIAAAKAIGASTPYILLREILPNIMGALIVVVTLEMAHAILLEATLSFLGLGVQPP 252 Query: 257 TPSWGLMVAEGKTYMFFKPWVIVIPGVALALLVLAINLVGDGLRDVNAPDGRN 309 TPSWGLMVAEGKTYMFFKPWVIVIPGVALALLVLAINLVGDGLRDVNAPDGRN Sbjct: 253 TPSWGLMVAEGKTYMFFKPWVIVIPGVALALLVLAINLVGDGLRDVNAPDGRN 305 >gi|300310894|ref|YP_003774986.1| dipeptide/oligopeptide/nickel ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 320 Score = 193 bits (491), Expect = 1e-50, Method: Compositional matrix adjust. Identities = 114/283 (40%), Positives = 174/283 (61%), Gaps = 5/283 (1%) Query: 28 WRRQLRRLLGHRGLMLGAAVLAVIVLAAIFAPLLAPHDPFD----QDVTARLIPPVWQAQ 83 WRR +R + R MLG ++ ++++ AI AP + P +P+D + ARL P Sbjct: 34 WRRVMRHFVASRSAMLGLVIVLLLIVGAIAAPWITPQNPYDLMQLDVLDARLHPGTLNGA 93 Query: 84 GSWEHILGTDKLGRDYLSRLIFGARVSLTIGVAAALISGLIGTTLGVLAGYFGGRTDAVI 143 G++ + LGTD GRD +S +++G R+S+ IGV +ALI+G+IGT +G+LA Y GG+ D ++ Sbjct: 94 GTYTYWLGTDGQGRDLVSAILYGLRISVGIGVGSALIAGVIGTLIGLLAAYAGGKLDTLL 153 Query: 144 SYLITTRLAMPVVLVALAMASLVGGSLKVVIVLLGLLLWDRFAVVTRSATQQLRDAEFIA 203 L+ P +LVA+ + + VG + V+ L +L W +A R R E++ Sbjct: 154 MRFADLVLSFPSILVAMLILAYVGKGIFNVMATLVVLEWAYYARTARGQALVERRKEYVE 213 Query: 204 AAKAIGASTPYILLREILPNIMGALIVVATLEMAHAILLEATLSFLGLGVQPPTPSWGLM 263 AA+ + S+ I++R ILPN + LIV+ TL++A AI LEATLSFLGLGV PS GL+ Sbjct: 214 AARGLNLSSWRIMVRHILPNCLPPLIVIGTLQVARAITLEATLSFLGLGVPITEPSLGLL 273 Query: 264 VAEGKTYMFF-KPWVIVIPGVALALLVLAINLVGDGLRDVNAP 305 ++ G YM + W+ PG+ L ++++AINLVGD LRD+ P Sbjct: 274 ISNGYQYMLSGEYWISFYPGITLLVVIVAINLVGDRLRDILNP 316 >gi|300311171|ref|YP_003775263.1| dipeptide/oligopeptide/nickel ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 310 Score = 181 bits (460), Expect = 5e-47, Method: Compositional matrix adjust. Identities = 104/281 (37%), Positives = 152/281 (54%), Gaps = 11/281 (3%) Query: 28 WRRQLRRLLGHRGLMLGAAVLAVIVLAAIFAPLLAPHDP---FDQDVTARLIPPVWQAQG 84 WR R+ + + +V AI AP + P DP FD D PP Sbjct: 33 WREFWRKFKKQHLAVYAGVFILFLVAVAILAPWIVPFDPENFFDYDALNS--PP------ 84 Query: 85 SWEHILGTDKLGRDYLSRLIFGARVSLTIGVAAALISGLIGTTLGVLAGYFGGRTDAVIS 144 +W H G D LGRD SR++ G R+SL G + I +IGT G+LAGY+ G D + Sbjct: 85 TWVHWFGVDSLGRDIFSRIVMGTRISLAAGFFSVAIGAVIGTVFGLLAGYYEGWWDRITM 144 Query: 145 YLITTRLAMPVVLVALAMASLVGGSLKVVIVLLGLLLWDRFAVVTRSATQQLRDAEFIAA 204 + A P +L+A+ + +++GG + VI+ + + FA + R T QL++ +I A Sbjct: 145 RICDVLFAFPGILLAIGIVAILGGGMINVIISVSVFSIPAFARLVRGNTLQLKNLTYIEA 204 Query: 205 AKAIGASTPYILLREILPNIMGALIVVATLEMAHAILLEATLSFLGLGVQPPTPSWGLMV 264 ++IGAS I+ + I P + A++V T+ + +I+ A LSFLGLG Q PTP WGLM+ Sbjct: 205 TRSIGASDMTIMWKHIFPGTISAIVVYFTMRIGTSIITAAGLSFLGLGAQSPTPEWGLML 264 Query: 265 AEGKTYMFFKPWVIVIPGVALALLVLAINLVGDGLRDVNAP 305 E + M P V ++P +A+ L VLA NL+GDGLRD P Sbjct: 265 NEARADMVTSPHVALVPSIAIFLTVLAFNLLGDGLRDALDP 305 >gi|300310465|ref|YP_003774557.1| dipeptide/oligopeptide/nickel ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 293 Score = 114 bits (285), Expect = 1e-26, Method: Compositional matrix adjust. Identities = 83/265 (31%), Positives = 145/265 (54%), Gaps = 12/265 (4%) Query: 43 LGAAVLAVIVLAAIFAPLLAPHDP---FDQDVTARLIPPVWQAQGSWEHILGTDKLGRDY 99 +G A++ +L AI P ++P+D D DV + + S + +LG+D LGRD Sbjct: 35 IGMAIVGFWILMAILGPSISPYDATAIVDTDVFSGM---------SHKFLLGSDYLGRDM 85 Query: 100 LSRLIFGARVSLTIGVAAALISGLIGTTLGVLAGYFGGRTDAVISYLITTRLAMPVVLVA 159 LSR++FG R ++ + +AA +++ GT + + A + GG DAVIS + +++P + A Sbjct: 86 LSRILFGTRATIGLALAATVLASATGTAIALFAAFSGGWRDAVISRALDALISIPSKMFA 145 Query: 160 LAMASLVGGSLKVVIVLLGLLLWDRFAVVTRSATQQLRDAEFIAAAKAIGASTPYILLRE 219 L M + G S+ ++++ + + RS ++ E++ AA+A G YI+ E Sbjct: 146 LMMVATFGSSMLLLVLTAAITYMPGAYRIARSLAVNVQAMEYVQAARARGEGVWYIMTVE 205 Query: 220 ILPNIMGALIVVATLEMAHAILLEATLSFLGLGVQPPTPSWGLMVAEGKTYMFFKPWVIV 279 +LPN++ ++ L + +LL + LSFL LGVQPP WG +V E + + ++ Sbjct: 206 MLPNMIRPVLADFGLRFVYVVLLLSGLSFLSLGVQPPDADWGSLVRENISGLGEGALAVI 265 Query: 280 IPGVALALLVLAINLVGDGLRDVNA 304 +P +A+A L + +NL+ D LR A Sbjct: 266 MPALAIASLTIGVNLLIDNLRSKRA 290 >gi|300312717|ref|YP_003776809.1| ABC transporter permease [Herbaspirillum seropedicae SmR1] Length = 348 Score = 112 bits (279), Expect = 5e-26, Method: Compositional matrix adjust. Identities = 70/183 (38%), Positives = 105/183 (57%) Query: 87 EHILGTDKLGRDYLSRLIFGARVSLTIGVAAALISGLIGTTLGVLAGYFGGRTDAVISYL 146 E+ LGTD GRD +RL++G RVS+ G+A I ++G G + GYF GRTD L Sbjct: 127 ENWLGTDDRGRDVFARLLYGFRVSVLFGMALTFIGVVLGVAAGAVQGYFAGRTDLFTQRL 186 Query: 147 ITTRLAMPVVLVALAMASLVGGSLKVVIVLLGLLLWDRFAVVTRSATQQLRDAEFIAAAK 206 + +MP + + + +S+ SL +++VLL L W + R+ + R+ E+I AA+ Sbjct: 187 LEIWGSMPELYLLIIFSSIFQPSLGLLLVLLSLFGWMSLSDYVRADFLRNRNLEYIQAAR 246 Query: 207 AIGASTPYILLREILPNIMGALIVVATLEMAHAILLEATLSFLGLGVQPPTPSWGLMVAE 266 A+G I+ R +LPN M ++ M+ AIL +L FLGLGV P TPS G ++A+ Sbjct: 247 AMGLPDRLIIWRHVLPNSMTTVVTFLPFRMSAAILALTSLDFLGLGVPPSTPSLGELLAQ 306 Query: 267 GKT 269 GK Sbjct: 307 GKN 309 Database: BlastDatabases/689/689 Posted date: Apr 10, 2011 12:15 AM Number of letters in database: 1,619,870 Number of sequences in database: 4735 Lambda K H 0.326 0.140 0.418 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 4735 Number of Hits to DB: 626,381 Number of extensions: 21755 Number of successful extensions: 170 Number of sequences better than 1.0e-08: 6 Number of HSP's gapped: 170 Number of HSP's successfully gapped: 6 Length of query: 309 Length of database: 1,619,870 Length adjustment: 85 Effective length of query: 224 Effective length of database: 1,217,395 Effective search space: 272696480 Effective search space used: 272696480 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 bits) S2: 130 (54.7 bits)